Don't use a separate /boot partition. FreeBSD is not Linux. Just use /.

If you (for whatever reason) decide you absolutely must have a separate /boot, then you will need to boot off a rescue CD, mount the / and /boot partitions, and edit /boot/loader.conf to point it at /kernel/kernel for the kernel instead of /boot/kernel/kernel (and the module path at /kernel instead of /boot/kernel, and any other paths that include /boot will have to be modified to remote /boot). All paths in the boot loader are relative to the partition that the loader is in.